1-230746016-C-T

Variant names:

• chr1-230746016-C-T
• rs10495300
• ENST00000412344.1:n.381-35163G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000412344.1(ENSG00000244137):​n.381-35163G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.197 in 152,088 control chromosomes in the GnomAD database, including 3,273 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.20 (3273 hom., cov: 31)
• Consequence: ENSG00000244137 ENST00000412344.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.426
• Publications: 2 publications found

Genes affected

ENSG00000244137 (HGNC:58238):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.253 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000244137	ENST00000412344.1	n.381-35163G>A		intron_variant	Intron 1 of 1	3

Frequencies

GnomAD3 genomes AF: 0.197 AC: 29926 AN: 151972 Hom.: 3273 Cov.: 31

Gnomad AFR AF: 0.137

Gnomad AMI AF: 0.176

Gnomad AMR AF: 0.170

Gnomad ASJ AF: 0.244

Gnomad EAS AF: 0.0195

Gnomad SAS AF: 0.0879

Gnomad FIN AF: 0.207

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.256

Gnomad OTH AF: 0.218

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.197 AC: 29930 AN: 152088 Hom.: 3273 Cov.: 31 AF XY: 0.190 AC XY: 14110 AN XY: 74336

African (AFR) AF: 0.137 AC: 5674 AN: 41494

American (AMR) AF: 0.170 AC: 2600 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.244 AC: 848 AN: 3470

East Asian (EAS) AF: 0.0191 AC: 99 AN: 5170

South Asian (SAS) AF: 0.0878 AC: 423 AN: 4818

European-Finnish (FIN) AF: 0.207 AC: 2182 AN: 10556

Middle Eastern (MID) AF: 0.170 AC: 50 AN: 294

European-Non Finnish (NFE) AF: 0.257 AC: 17439 AN: 67984

Other (OTH) AF: 0.216 AC: 455 AN: 2110

Alfa AF: 0.210 Hom.: 2556

Bravo AF: 0.194

Asia WGS AF: 0.0690 AC: 242 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	9.1
DANN	Benign	0.80
PhyloP100		0.43
PromoterAI		-0.0040	Neutral

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs10495300; hg19: chr1-230881762; COSMIC: COSV55231842;